According to Stan Lee, one of the reasons Spider-Man wears a mask is so his enemies can't see when he's afraid. It truly shows how human and vulnerable Spider-Man is.
Aunt May's death in Amazing Spider-Man #400 is widely considered a perfect, poignant sendoff for the character. She spends her final weeks with Peter and Mary Jane, telling them how proud she is of both of them and expressing hope and love for their unborn child. When she develops a fever and becomes tired Peter is concerned, but she brushes off doctors because she can feel it's her time. Her deathbed scene has Peter quoting from Peter Pan as she dies, Ben Reilly is also seen crying, and the comic ends with her tombstone next to Uncle Ben's, with the inscription "She taught us love."
The mini comic "Leah".◊ What makes it even more of a tear jerker is that the writer made it in remembrance of a friend. The story is inspired from The Little Matchgirl, so the tearjerker has to be expected. It also combines with heartwarming, though, that instead of Dying Alone, Leah falls into a coma alone and she's found by Spidey who immediately takes her to the hospital. But the doctor informs him that the girl won't make it. Spidey kisses her on the cheek while wishing "Sweet dreams, Leah." Later, we are shown that while dying, Leah has a Dying Dream where she and Spider-Man go into adventure along with many other Marvel heroes, among them includes Iron Man, Ms. Marvel, Silver Surfer, Thor and even the Sub-Mariner. The words on the last panel take it all, "Sweet. Sweet Dreams."
"The Kid Who Collects Spider-Man," in which Spider-Man visits Tim, a nine year old fan. The story's heartwarming enough already (especially when Spidey shows Tim his secret identity), but what really gets readers is the revelation at the end that Tim was diagnosed with cancer and given a few weeks to live.
While it happened much earlier, the death of Captain Stacy also hits the waterworks. Considering how Cap. Stacy had shown to be an ally to Spidey, this death hit him very hard. Especially considering how Gwen is completely on her own now due to it, she hates Spider-Man with all her being due to thinking he killed her father, and Peter carrying even more guilt than usual (and not even being able to tell his girlfriend he is Spider-Man).
"Maybe Next Year" is an issue about Peter remembering his Uncle Ben's tradition of taking him out to a Mets baseball game. Since it's the Mets, they never win, but Uncle Ben always tells Peter they have to keep cheering...
The water works increase by the end. The last game he went to with Ben reveals that for once the their team actually wins, which causes an excited Peter to finally understand Ben's message of always supporting the team no matter what... And then after this heartwarming moment the narration reveals that this all takes place just three days before Ben's murder.
One More Day. When Peter and Mary Jane are about to lose their memories, Mary Jane says this:
Mary Jane: Peter, whatever he [Mephisto] does or undoes, it doesn't matter. Because whatever he does to pull us apart would have to be stronger and bigger than what brought us together and kept us together, no matter what happened. And there is no power in the universe big enough for a job like that. Not the devil, not god, not ANYONE. We will find each other and be together again.
In ASM #700, Peter dying in Doc Ock's body.
It gets worse - no-one, not Peter's friends & family or the rest of the Avengers, knows the switch happened. Aunt May & Mary Jane watched Peter die & didn't realise it.
In issue 9 of Superior Spider-Man, Otto erases Ghost-Peter and all his memories after a No-Holds-Barred Beatdown and (arguably true) "The Reason You Suck" Speech. Peter is destroyed after losing all his memories: of Uncle Ben, of Captain Stacy, he even forgets HIS OWN NAME.
Peter Parker: Spider Man Volume 2, #25. The comic begins with a nightmare many people have had: Peter being trapped in a coffin, buried six feet under. While it's a hallucination, the truth isn't all that much better. Peter is currently being held captive and tortured by Norman towards some sinister end. As the issue goes on, it becomes clear that Norman isn't just doing this out of some sadistic need to torment his arch nemesis. He wants to make Peter join him as the next goblin, to get him to reject the light and instead accept the darkness, and the goblin formula. And he succeeds. Peter breaks. Despite a last minute vision of Aunt May keeping from actually drinking the formula, he still accepted it, and this is something Norman doesn't let Peter forget.
In Spectacular #200, Harry in Green Goblin gear abducts MJ and takes her to the bridge for a little talk. MJ accuses Harry of wanting to push her off like Norman did to Gwen. Harry takes offense and reveals how much Gwen's death has affected him.
"You know... I still miss Gwen. So much. There are times... even after all these years... when I just can't believe it. 'It can't be true,' I think. 'She can't really be dead.'"
The last two pages of the story, where dialogue-less panels depict Harry dying and Spidey breaking the news.
As Harry is dying after snapping out of the Goblin persona and saving Peter, Peter asks him why he did it, and Harry gasps out his last words: "How could I not, Pete? You're my best friend." And much like Aunt May's death, the company saw fit to taint this moment, only this one with one nasty Thanatos Gambit.
Yes it's part of The Clone Saga but that doesn't stop the 3-issue miniseries Spider-Man: The Lost Years from being this. Kaine gets it the worst though when his clone degeneration accelerates at the same time he finds out Louise Kennedy, the woman he'd fallen in love with, was really a Dirty Cop which is enough to make him snap.
"Even then I wanted to call out to her... beg her not to leave me. But I'd humiliated myself enough. Even Professor Warren hadn't made me feel so small, so... ridiculous. Then why did I cling to these feelings; exult in them? Why did I drink from my cup of shame slowly... relishing each small sip? Perhaps because the source of my shame was her. The only love I'd ever known. The only love I ever would know. And I wanted to savor even the dregs of that love... before I destroyed her."
If you can get past the whole Mary Jane dying because of radioactive cells from having sex with Peter, then the Spider-Man: Reign story can actually be quite sad, like when Doctor Octopus gives the original Spider-Man costume back to a crushed Peter Parker, but Doctor Octopus was already dead, trying to find Peter so that he could bring the age of Super Heroes back, he put a recorded message into his arms to deliver this.
What happens to Sandman's daughter. He wasn't even aware of her existence, and he only realizes her true identity right before she's murdered by the Mayor's thugs. His horror and grief at her fate is what ultimately gives him the strength to rebel and help Spider-Man defeat Venom and rid New York of its fascist regime.
In a way, Venom. It is outright stated that Eddie and the symbiote have clearly truly become one being - Venom, but what is especially notable is how much more vile he is in this story, having entirely foregone any shred of antiheroism in favor in destroying the city Spider-Man fought for many years, out of sheer pettiness over being rejected. The tearjerking part of it is that...what made him snap? He could have easily started off normally, having put aside his feud with Spider-Man to fight criminals himself, but then years later, something had made him turn away so hostilely; to become the utter monster he is here. Whatever happened to Reign's Venom to make him this way must have been beyond soul-crushing, and yet still not enough to justify what he does in this story.
Even his debut ends with one: Uncle Ben's death.
Peter: My fault... All my fault... Because I didn't stop that punk when I could have! Now Uncle Ben is dead! He's dead!!!
Amazing Spider-Man 657, particularly the last page. This is right after Johnny Storm's death and Peter's going to mourn with the Fantastic Four. The whole comic alternates between being a tearjerker and a Funny Moment, but it ends on a particularly tearjerking note with Peter watching Johnny Storm's video-will of sorts, in which Johnny not only gives Peter his spot on the team, but his spot in the Fantastic Four family.
Johnny: If youre hearing this, Im sorry, pal. Sorry that Im gone. Cause... well... I know how you feel when it comes to losing family. And thats what you are to me. Family. So... if youre thinking of this as my last will and all... Im not leaving you my sports cars or stuff like that... Im leaving you the best thing I ever had... My spot on this team. A place in this family. The best sister, two brothers, niece, and nephew a guy could ask for. They— We all love you, Pete. So? You up for it, bro? Were all here for you.
"The Final Curtain" from Spectacular Spider-Man #27. It starts with Peter visiting Uncle Ben's grave on Christmas Day to have a chat with his ghost and wish him Happy Holidays, and it slowly slips into Peter sharing a recurring nightmare about finally being defeated by his foes, all interspersed with flashbacks of a seven year-old Peter freezing up on stage during a class play. Peter comes clean about all of the crushing fears and insecurities that he deals with every day when facing his Rogues' Gallery... and it gets all the more heartbreaking when Uncle Ben pointedly tells him, at one point, that he's not really there, and that Peter's just talking to himself. In the end, there's no one with whom Peter can be this honest about how much being Spider-Man scares him, but he still puts up with it every day, because, well... it's his responsibility.
During this arc, Peter Parker is unemployed and being battered by his classic enemies. The only good thing to come out of everything is that Aleksei Sytsevich, the Rhino, had married and reformed. When the new Rhino kills Aleksei's wife, Spider-Man desperately pleads and struggles in vain to keep Aleksei from becoming the Rhino again and is left with nothing but fear and loneliness when he fails.
A sound comes out of Spider-Man that's so soft it screams. It's the sound of his heart breaking.
Another case of Tear Jerker, mixed with horror for good measure appears when Curt Connor loses control of his Super-Powered Evil Side and kills his son Billy. It's horrifying and heartbreaking because it depicts a father losing control of himself and killing his own child. Even worse, the experience essentially destroys "Curt" as well, leaving the Lizard in charge. What makes it even worse is Billy's last words: "You're going to kill me, aren't you? I knew it..."
Little Keemia screams at Spider-Man that she hates him. He'd gotten involved in a murder case when a friend of his was implicated for screwing up the evidence, to find that the victims, a woman and her lawyer, were involved in an acrimonious fight with Flint Marko, the Sandman. She'd been snowing him into believing he had a daughter, even though it was no longer physically possible for him to have a child, and he'd become so obsessed with trying to be a good father that a part of himself had split off and killed them in order to get them out of the way without him even being aware of it. Spider-Man defeats him and gets the girl back, but because her grandmother (who had been her caretaker when Marko took her) admitted she wasn't watching the child when she was taken, CPS is putting her in the foster system, after Spider-Man had promised her she'd be with her family in order to make her go with him. Not knowing what happened to her mother, Keemia had thought her "father" was a good father, and so having lost everything as a result of leaving him, views Spider-Man as a liar and a thief.
From Webspinners - Tales of Spider-Man comes The Show Must Go On, wherein Spider-Man's first supervillain the Chameleon has a breakdown after trying to start a new life. He goes to a circus and becomes a clown named Eugene and, although he likes his new life and the person he's become, finds that he is still unable to fully rid himself of his past, even if only in his head. He pretends that he's holding MJ hostage on a bridge in order to draw out Spider-Man into meeting him so that they can hopefully talk. They discuss what drove Chameleon into giving up his new, happy life, getting personal with Peter's mask off and Chameleon asking to be called by his first name Dmitri. Chameleon finally is able to work himself up into confessing what's really been driving him into despair: that he loves Peter. Peter, out of shock rather than out of mocking, laughs. Chameleon, although trying to brush it off and act like he was joking and even joining in on Peter's laughter, is clearly crushed. Seriously, his face after Peter starts laughing is heartbreaking. Not to mention when he softly says, "Stop it..." in a way that could be construed as telling Peter to stop making him laugh, but is clearly actually him begging for Peter to stop laughing. And Peter never meant to laugh, it was his reaction to the shock of Chameleon's confession, not any malice. After they finally stop, Chameleon hands over the gun he was holding to Peter, telling him that he was glad he could make him smile and that he looks nice when he does. Chameleon then proceeds to fold his arms over his chest, smile peacefully, and falls off of the bridge. Although Peter quickly dives him afterwards, horrified that he's accidentally driven a man to suicide and in a similar manner to how Gwen Stacy died, he's too late and Chameleon hits the water. Chameleon wound up surviving this, but it's still one of the most tearjerking moments in any Spider-Man comic.
Spider-Man and Mary Jane were happy that they will be parents. However, the Green Goblin had MJ poisoned which killed her unborn baby. Mary Jane not hearing any crying from her daughter kept asking why is her daughter not crying and the doctor looking at her seemingly not know how to tell her that her daughter is dead. When Peter arrive all that he could do was hug his wife as they both cry.
Much later, the nurse who poisoned MJ on the Goblin order said that May is alive. Spider-Man is convinced that the said May is his daughter while Mary Jane try to tell him that it could be a trick but he doesn't listen and leave to the place where he thinks he daughter is being held. He fights the Goblin who admitted that he didnt take his daughter as she is dead, but Peter doesn't believe him and shout at him to stop lying and defeat him then he enter the place looking for his daughter completely convincedthat he will find her there only for someoneto hit him on the back of his head. Spidey turn and see that it is his aunt May who was replaced with an actress that was injected with her DNA. At that moment he realised that his daughter is really, really dead. Spidey gives a Big "NO!" as his nemesis laughing at him outside.
A relatively small one, but in Marvel Team-Up #6 (2005), X-23 not only makes it clear to Spidey that she can't stand him, but that, to his shock, every other hero feels the same way. What makes it worse is to hear Captain America, of all people, express this opinion, even if only to a minor extent. Sure, Peter is often the cause of his own reputation, but you still can't help feeling sorry for the poor guy ◊.
"The Death of Jean DeWolffe" hits Peter pretty hard. Jean was usually Brutally Honest towards Spider-Man, but she was still one of his defenders and friends. Readers had previously learned she actually had a crush on Spidey, which Peter discovers when going through her things and finding pictures of himself.
"Was she doing some sort of study on me? No, she would have kept that at her office. She kept these because she liked them. But... she never said anything particularly warm to me. Heck, she usually chewed me out. It can't be. She couldn't have cared for me. Why didn't she ever say anything if she felt... we could have... It can't be true. She was always so cool, so aloof. Blast it, why did she have to be that way?"
Mary Jane's backstory, as seen in Amazing Spider-Man issue 257 and the one-shot Parallel Lives. Coming from a broken home with an abusive father, a dying mother and a put upon sister, it's heartbreaking (yet understandable) how MJ left that world of baggage to focus on her dreams.
Flash Thompson's death. After many decades of character development, starting off as a Jerk Jock bully towards Peter and slowly evolving into a Guile Hero in the form of Agent Venom, and then Anti-Venom, he performs a Heroic Sacrifice against the Red Goblin and encourages Peter to finish the fight they started, even calling Peter his hero and friend; words that Peter solemnly returns in his funeral. While it proves to show that Peter's life may always be filled with tragedy, this scene, as well as Flash's funeral, is also a beautiful sendoff to a longtime supporting character, and, as a hero, a beloved Ensemble Dark Horse.
In issue 310 of Peter Parker: The Spectacular Spider-Man a film student is making a documentary about Spider-Man with the interviews consisting of people sharing their opinions and encounters with Spider-Man. However one woman shares the story of how her son was the lookout for to criminals robbing a store. While Spider-Man caught the two criminals he let the boy go. The story goes on a heartwarming path as she shares how after that her son did a complete 180 even doing better in school thanks to Spidey helping him with his math. Later on however she reveals the two criminals her son was a lookout for got out on bail and blamed him for them getting caught and murdered him. Spider-Man proceeds to capture the criminals and leave them for police then takes off his mask a cries. A heart wrenching reminder just how Peter with all his powers is still just human.
Peter Parker, The Spectacular Spider-Man #6 has a heartbreaking moment for J. Jonah Jameson, who interviews Spider-Man since the latter needs information on his assumed sister Teresa. The two go back-and-forth at each other, until Jameson realizes he's lost everything in his life—his job at the Bugle, his mayorship, his wife, and his self-respect, and hating Spider-Man is the only reason he can go on. Peter then reveals his identity to Jameson, telling him You Are Not Alone and that he's entrusting him with his secret.
A side story to The Hunted story arc follows the point of view of minor villain The Gibbon. From his childhood where he was relentlessly bullied, to the seemingly endless Trauma Conga Line that followed throughout his entire life. All while trying to escape an army of violent hunters who brutally harm him shortly after he was betrayed by Vulture. The issue ends with Spider-Man finding him and hopelessly trying to keep him alive. As Peter watches Gibbon die in his arms, the later, unable to speak, mentally curses himself for the long string of missteps that brought him to this end. His last thought before dying, finding some joy in the fact that he no longer hears anyone laughing at him.